Autophagy in wine making.

Abstract:

:Aging that involves contact with dying yeast cells is one of the differential processes between sparkling and still wine production. The release of the products of autolysis during this aging step is fundamental for the quality of sparkling wines made by the traditional method. These cells undergo an autolysis process characterized by self-digestion of yeast intracellular and cell-wall macromolecules, and the release of the degradation products to the wine. Autolysis is the source of several molecules responsible for the quality of sparkling wines, as well as still wines aged on lees (yeast cells). Autolysis is a slow process under sparkling wine production conditions, and there is interest, from the industrial side, in the design of strategies for rapid development of autolysis. Some years ago our research group hypothesized that, during the process of sparkling wine production, autophagy would take place. This had important implications for the design of genetic engineering strategies aimed to accelerate autolysis. The relationships between autolysis and autophagy are not completely elucidated, but in case autophagy preceded autolysis during the aging step of sparkling wine production, there were at least two possibilities for accelerating autolysis by targeting genes involved in autophagy. This chapter discusses methods to demonstrate the development of autophagy under enological conditions. This is accomplished by using either laboratory strains defective in autophagy and/or the Cvt pathway, in conditions that mimic sparkling wine production or industrial wine yeast strains under real sparkling wine production conditions.

journal_name

Methods Enzymol

journal_title

Methods in enzymology

authors

Cebollero E,Rejas MT,González R

doi

10.1016/S0076-6879(08)03212-6

subject

Has Abstract

pub_date

2008-01-01 00:00:00

pages

163-75

eissn

0076-6879

issn

1557-7988

pii

S0076-6879(08)03212-6

journal_volume

451

pub_type

杂志文章
  • Coomassie blue staining.

    abstract::This protocol describes Coomassie brilliant blue staining, one of the most common methods of detecting proteins in polyacrylamide gels (PAGE). ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-420119-4.00013-6

    authors: Brunelle JL,Green R

    更新日期:2014-01-01 00:00:00

  • General protein-protein cross-linking.

    abstract::This protocol describes a general protein-to-protein cross-linking procedure using the water-soluble amine-reactive homobifunctional BS(3) (bis[sulfosuccinimidyl] suberate); however, the protocol can be easily adapted using other cross-linkers of similar properties. BS(3) is composed of two sulfo-NHS ester groups and ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-420120-0.00006-2

    authors: Alegria-Schaffer A

    更新日期:2014-01-01 00:00:00

  • Chapter 4. Analyzing the regulation of antibiotic production in streptomycetes.

    abstract::This chapter outlines the approaches and techniques that can be used to analyze the regulation of antibiotic production in streptomycetes. It describes how to isolate antibiotic nonproducing and overproducing mutants by UV, nitrosoguanidine (NTG), transposon, and insertion mutagenesis, and then how to use those mutant...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(09)04804-6

    authors: Bibb M,Hesketh A

    更新日期:2009-01-01 00:00:00

  • Chapter 11 Supercomplex organization of the yeast respiratory chain complexes and the ADP/ATP carrier proteins.

    abstract::The enzymes involved in mitochondrial oxidative phosphorylation (OXPHOS) are coassembled into higher ordered supercomplexes within the mitochondrial inner membrane. The cytochrome bc(1)-cytochrome c oxidase (COX) supercomplex is formed by the coassociation of the two electron transport chain complexes, the cytochrome ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(08)04411-X

    authors: Stuart RA

    更新日期:2009-01-01 00:00:00

  • Prediction of alpha helices and T cell-presented sequences in proteins with algorithms based on strip-of-helix hydrophobicity index.

    abstract::Recurrent aliphatic hydrophobic amino acids which occur in the sequence of a protein or a peptide at positions which form an axial, hydrophobic strip when the sequence is coiled as an alpha helix might stabilize coiling against hydrophobic surfaces. That effect can lead to helix formation against hydrophobic cores of ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/0076-6879(91)02013-y

    authors: Reyes VE,Lew RA,Lu S,Humphreys RE

    更新日期:1991-01-01 00:00:00

  • Tagged Chromosomal Insertion Site System: A Method to Study Lamina-Associated Chromatin.

    abstract::The three-dimensional (3D) organization of the genome is important for chromatin regulation. This organization is nonrandom and appears to be tightly correlated with or regulated by chromatin state and scaffolding proteins. To understand how specific DNA and chromatin elements contribute to the functional organization...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2015.09.028

    authors: Harr JC,Reddy KL

    更新日期:2016-01-01 00:00:00

  • Recursive construction and error correction of DNA molecules and libraries from synthetic and natural DNA.

    abstract::Making error-free, custom DNA assemblies from potentially faulty building blocks is a fundamental challenge in synthetic biology. Here, we show how recursion can be used to address this challenge using a recursive procedure that constructs error-free DNA molecules and their libraries from error-prone synthetic oligonu...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-385120-8.00010-3

    authors: Yehezkel TB,Linshiz G,Kaplan S,Gronau I,Ravid S,Adar R,Shapiro E

    更新日期:2011-01-01 00:00:00

  • Sequence-specificity and energy landscapes of DNA-binding molecules.

    abstract::A central goal of biology is to understand how transcription factors target and regulate specific genes and networks to control cell fate and function. An equally important goal of synthetic biology, chemical biology, and personalized medicine is to devise molecules that can regulate genes and networks in a programmab...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-385075-1.00001-9

    authors: Tietjen JR,Donato LJ,Bhimisaria D,Ansari AZ

    更新日期:2011-01-01 00:00:00

  • Catalytic mechanisms and regulation of protein kinases.

    abstract::Protein kinases transfer a phosphoryl group from ATP onto target proteins and play a critical role in signal transduction and other cellular processes. Here, we review the kinase kinetic and chemical mechanisms and their application in understanding kinase structure and function. Aberrant kinase activity has been impl...

    journal_title:Methods in enzymology

    pub_type: 杂志文章,评审

    doi:10.1016/B978-0-12-397918-6.00001-X

    authors: Wang Z,Cole PA

    更新日期:2014-01-01 00:00:00

  • Using computational techniques in fragment-based drug discovery.

    abstract::Fragment-based drug discovery has emerged over the past 15 years as an effective lead discovery paradigm that is complementary to traditional high-throughput screening. The starting point for fragment-based drug discovery is the identification of low-molecular weight, typically low-affinity compounds that bind to a ta...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-381274-2.00006-6

    authors: Desjarlais RL

    更新日期:2011-01-01 00:00:00

  • Isolation and identification of neuroendocrine peptides from milk.

    abstract::Hormone, hormone-like substances, and neuroendocrine peptides are natural constituents of milk, and they may have an important physiological and pharmacological role in neonate development. The concentration of these peptides in milk greatly exceeds those in serum and implies an active concentration mechanism in the m...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/0076-6879(89)68038-x

    authors: Hazum E

    更新日期:1989-01-01 00:00:00

  • Mammalian glycosylphosphatidylinositol-anchored proteins and intracellular precursors.

    abstract::Glycosylphosphatidylinositol-anchored proteins can be specifically identified by several methods. PI-PLC digestion analyses, the most widely used technique, can be performed more reliably when conducted with purified protein and phase partitioning to exclude steric effects and when combined with alkaline hydrolysis to...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/0076-6879(95)50099-5

    authors: Hirose S,Knez JJ,Medof ME

    更新日期:1995-01-01 00:00:00

  • Dynamic imaging of homo-FRET in live cells by fluorescence anisotropy microscopy.

    abstract::Multiple lipid and protein components of the plasma membrane of a living cell are organized, both compositionally and functionally, at different spatial and temporal scales. For instance, Rab protein domains in membranes the clathrin-coated pit, or the immunological synapse are exquisite examples of functional compart...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-388448-0.00024-3

    authors: Ghosh S,Saha S,Goswami D,Bilgrami S,Mayor S

    更新日期:2012-01-01 00:00:00

  • Purification and analysis of the decapping activator Lsm1p-7p-Pat1p complex from yeast.

    abstract::Biochemical analysis of the components of the mRNA decay machinery is crucial to understand the mechanisms of mRNA decay. The Lsm1p-7p-Pat1p complex is a key activator of decapping in the 5' to 3'-mRNA decay pathway that is highly conserved in all eukaryotes. The first step in this pathway is poly(A) shortening that i...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(08)02603-7

    authors: Tharun S

    更新日期:2008-01-01 00:00:00

  • Molecular and stable isotope methods to detect and measure anaerobic ammonium oxidation (anammox) in aquatic ecosystems.

    abstract::Numerous microbial processes transform nitrogen (N) but three anaerobic respiratory pathways remove fixed N from the environment: denitrification (nitrate conversion to N(2)), anaerobic ammonium oxidation (anammox; ammonium plus nitrite conversion to N(2)), and nitrite dependent methane oxidation (nitrite conversion t...

    journal_title:Methods in enzymology

    pub_type: 杂志文章,评审

    doi:10.1016/B978-0-12-386489-5.00003-8

    authors: Song B,Tobias CR

    更新日期:2011-01-01 00:00:00

  • Gene expression of gamma-glutamyltranspeptidase.

    abstract::gamma-Glutamyltranspeptidase is a heterodimeric glycoprotein that catalyzes the transpeptidation and hydrolysis of the gamma-glutamyl group of glutathione and related compounds. It is known that the enzyme plays a role in the metabolism of glutathione and in salvaging constituents of glutathione. In the adult animal, ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章,评审

    doi:10.1016/S0076-6879(05)01025-6

    authors: Ikeda Y,Taniguchi N

    更新日期:2005-01-01 00:00:00

  • Dissecting the mechanisms of the clock in Neurospora.

    abstract::The circadian clock exists to synchronize inner physiology with the external world, allowing life to anticipate and adapt to the continual changes that occur in an organism's environment. The clock architecture is highly conserved, present in almost all major branches of life. Within eukaryotes, the filamentous fungus...

    journal_title:Methods in enzymology

    pub_type: 杂志文章,评审

    doi:10.1016/bs.mie.2014.10.009

    authors: Hurley J,Loros JJ,Dunlap JC

    更新日期:2015-01-01 00:00:00

  • Scanning FCS for the characterization of protein dynamics in live cells.

    abstract::Scanning fluorescence correlation spectroscopy (sFCS) is the generic term for a group of fluorescence correlation techniques where the measurement volume is moved across the sample in a defined way. The introduction of scanning is motivated by its ability to alleviate or remove several distinct problems often encounte...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(10)72005-X

    authors: Petrásek Z,Ries J,Schwille P

    更新日期:2010-01-01 00:00:00

  • Advances in phylogeny reconstruction from gene order and content data.

    abstract::Genomes can be viewed in terms of their gene content and the order in which the genes appear along each chromosome. Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide sequences) and have been advocated by systematists for...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(05)95035-0

    authors: Moret BM,Warnow T

    更新日期:2005-01-01 00:00:00

  • Epitope tagging and protein surveillance.

    abstract::The epitope tagging approach offers advantages of economy, universality, and precision over the use of antibodies raised directly against a protein of interest. The latter strategy promises a potentially greater diversity of reagents and obviates the need to modify the protein, but it may not yield sufficiently high-a...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/0076-6879(91)94038-e

    authors: Kolodziej PA,Young RA

    更新日期:1991-01-01 00:00:00

  • Assays for functional properties of Rab34 in macropinosome formation.

    abstract::We have shown that Rab34/Rah participates in the promotion of macropinosome formation. Here we describe procedures for the analyses of intracellular localization and some functional properties of Rab34. Rab34 lacks a consensus sequence of the fourth motif for GTP/GDP binding and GTPase activities. Indeed, GTPase assay...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(05)03019-3

    authors: Sun P,Endo T

    更新日期:2005-01-01 00:00:00

  • Affinity Purification of a Recombinant Protein Expressed as a Fusion with the Maltose-Binding Protein (MBP) Tag.

    abstract::Expression of fusion proteins such as MBP fusions can be used as a way to improve the solubility of the expressed protein in E. coli (Fox and Waugh, 2003; Nallamsetty et al., 2005; Nallamsetty and Waugh, 2006) and as a way to introduce an affinity purification tag. The protocol that follows was designed by the authors...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2014.11.004

    authors: Duong-Ly KC,Gabelli SB

    更新日期:2015-01-01 00:00:00

  • On-pot and cell-free biocatalysis using coimmobilized enzymes on advanced materials.

    abstract::Complex synthetic schemes catalyzed by multienzyme systems immobilized on solid materials are gaining momentum in chemical biomanufacturing. These systems harness the high chemo-, regio-, and stereoselectivity of the enzymes and the recyclability of the heterogeneous catalysts. Moreover, when the enzymes become part o...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2018.12.013

    authors: López-Gallego F

    更新日期:2019-01-01 00:00:00

  • RNA folding during transcription: protocols and studies.

    abstract::RNA folds during transcription in the cell. Compared to most in vitro studies where the focus is generally on Mg(2+)-initiated refolding of fully synthesized transcripts, cotranscriptional RNA folding studies better replicate how RNA folds in a cellular environment. Unique aspects of cotranscriptional folding include ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(09)68009-5

    authors: Wong TN,Pan T

    更新日期:2009-01-01 00:00:00

  • Application of mesoporous silica nanoparticles in intracellular delivery of molecules and proteins.

    abstract::Delivery of drugs and molecules to eukaryote animal and plant cells can be enhanced when mediated by mesoporous silica nanoparticle (MSN) materials. This chapter describes, in detail, the synthesis of several different MSN materials used for the transport of various hydrophilic and hydrophobic drug molecules, neurotra...

    journal_title:Methods in enzymology

    pub_type: 杂志文章,评审

    doi:10.1016/B978-0-12-391860-4.00003-3

    authors: Fang IJ,Trewyn BG

    更新日期:2012-01-01 00:00:00

  • Biochemical Characterization of Function and Structure of RseP, an Escherichia coli S2P Protease.

    abstract::Intramembrane-cleaving proteases (I-CLiPs) are a group of membrane-associated proteases with a unique feature: they are believed to cleave their substrate within the hydrophobic lipid bilayer, even though peptide bond hydrolysis requires a water molecule. Escherichia coli RseP, which belongs to the S2P zinc metallopro...

    journal_title:Methods in enzymology

    pub_type: 杂志文章,评审

    doi:10.1016/bs.mie.2016.09.044

    authors: Hizukuri Y,Akiyama K,Akiyama Y

    更新日期:2017-01-01 00:00:00

  • CXCR4 and mobilization of hematopoietic precursors.

    abstract::The binding of the chemokine [C-X-C motif] ligand 12 (CXCL12 or stromal cell-derived factor 1alpha [SDF-1alpha]) constitutively produced by bone marrow stromal cells and osteoblasts, to the CXC receptor (CXCR) 4, a transmembrane chemokine receptor expressed on hematopoietic stem and progenitor cells (HSPCs), has emerg...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(09)05203-3

    authors: Rettig MP,Ramirez P,Nervi B,DiPersio JF

    更新日期:2009-01-01 00:00:00

  • CRISPR-Cas molecular beacons as tool for studies of assembly of CRISPR-Cas effector complexes and their interactions with DNA.

    abstract::CRISPR-Cas systems protect prokaryotic cells from invading phages and plasmids by recognizing and cleaving foreign nucleic acid sequences specified by CRISPR RNA spacer sequences. Several CRISPR-Cas systems have been widely used as tool for genetic engineering. In DNA-targeting CRISPR-Cas nucleoprotein effector comple...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2018.10.026

    authors: Mekler V,Kuznedelov K,Minakhin L,Murugan K,Sashital DG,Severinov K

    更新日期:2019-01-01 00:00:00

  • Human embryonic stem cells.

    abstract::Human embryonic stem cells hold great promise in furthering our treatment of disease and increasing our understanding of early development. This chapter describes protocols for the derivation and maintenance of human embryonic stem cells. In addition, it summarizes briefly several alternative methods for the culture o...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(06)18005-2

    authors: Akutsu H,Cowan CA,Melton D

    更新日期:2006-01-01 00:00:00

  • Exploration of self-renewal and pluripotency in ES cells using RNAi.

    abstract::Embryonic stem cells (ESCs) have the ability to expand indefinitely in vitro and give rise to cells of all three germ layers as well as germ cells. For these reasons, ESCs hold great promise for biomedicine. In order to harness the potential of pluripotent cells, it is necessary to first understand the molecular mecha...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(10)77018-X

    authors: Schaniel C,Lee DF,Lemischka IR

    更新日期:2010-01-01 00:00:00